Commit c7717d8c authored by Pradat Yoann's avatar Pradat Yoann
Browse files

remove gitlab ci; add badges

parent b4784d84
image: "python:3.9"
default:
tags:
- docker
stages:
- test
variables:
CODECOV_TOKEN: "c8bcf054-f0cb-4bf1-8866-1b862905ef89"
before_script:
- make install
test:
stage: test
script:
- make test
- bash <(curl -s https://codecov.io/bash)
only:
refs:
- master
......@@ -24,6 +24,9 @@ test:
$(PIP) install --upgrade pytest pytest-cov
$(PYTEST) --cov-config=.coveragerc --cov-report term-missing --cov . .
codecov:
bash <(curl -s https://codecov.io/bash) -t c8bcf054-f0cb-4bf1-8866-1b862905ef89
build:
@echo "---------------Build variant_annotator-----------------"
$(PYTHON) -m pip install --user --upgrade setuptools wheel
......
# Biotool for annotating variants from a VCF file.
[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
[![codecov](https://codecov.io/gh/ypradat/VariantAnnotator/branch/master/graph/badge.svg?token=H821S3WZHS)](https://codecov.io/gh/ypradat/VariantAnnotator)
The tool is divided in 3 steps
- Manual parsing of the VCF
- Run [vcf2maf](https://github.com/mskcc/vcf2maf) to extract standard information
......@@ -7,7 +10,7 @@ The tool is divided in 3 steps
## 1. What is the tool doing ?
VEP annotates variants with information from multiple external databases and can be configure for to answer a lot of
VEP annotates variants with information from multiple external databases and can be configured to answer a lot of
specific needs. For more details, see [VEP's options
page](https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html). VEP does not however extract information
like number of reads or somatic status from the VCF file. vcf2maf is supposed to perform these tasks but failed to do on
......
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n_GT n_SS n_TIR n_TAR n_DP n_DP4 n_AD n_depth n_ref_count n_alt_count t_GT t_SS t_TIR t_TAR t_DP t_DP4 t_AD t_depth t_ref_count t_alt_count Variant_Quality Filter_VCF Hugo_Symbol_VCF2MAF Entrez_Gene_Id_VCF2MAF Center_VCF2MAF NCBI_Build_VCF2MAF Chromosome_VCF2MAF Start_Position_VCF2MAF End_Position_VCF2MAF Strand_VCF2MAF Variant_Classification_VCF2MAF Variant_Type_VCF2MAF Reference_Allele_VCF2MAF Tumor_Seq_Allele1_VCF2MAF Tumor_Seq_Allele2_VCF2MAF dbSNP_RS_VCF2MAF dbSNP_Val_Status_VCF2MAF Tumor_Sample_Barcode_VCF2MAF Matched_Norm_Sample_Barcode_VCF2MAF Match_Norm_Seq_Allele1_VCF2MAF Match_Norm_Seq_Allele2_VCF2MAF Tumor_Validation_Allele1_VCF2MAF Tumor_Validation_Allele2_VCF2MAF Match_Norm_Validation_Allele1_VCF2MAF Match_Norm_Validation_Allele2_VCF2MAF Verification_Status_VCF2MAF Validation_Status_VCF2MAF Mutation_Status_VCF2MAF Sequencing_Phase_VCF2MAF Sequence_Source_VCF2MAF Validation_Method_VCF2MAF Score_VCF2MAF BAM_File_VCF2MAF Sequencer_VCF2MAF Tumor_Sample_UUID_VCF2MAF Matched_Norm_Sample_UUID_VCF2MAF HGVSc_VCF2MAF HGVSp_VCF2MAF HGVSp_Short_VCF2MAF Transcript_ID_VCF2MAF Exon_Number_VCF2MAF t_depth_VCF2MAF t_ref_count_VCF2MAF t_alt_count_VCF2MAF n_depth_VCF2MAF n_ref_count_VCF2MAF n_alt_count_VCF2MAF all_effects_VCF2MAF Allele_VCF2MAF Gene_VCF2MAF Feature_VCF2MAF Feature_type_VCF2MAF Consequence_VCF2MAF cDNA_position_VCF2MAF CDS_position_VCF2MAF Protein_position_VCF2MAF Amino_acids_VCF2MAF Codons_VCF2MAF Existing_variation_VCF2MAF ALLELE_NUM_VCF2MAF DISTANCE_VCF2MAF STRAND_VEP_VCF2MAF SYMBOL_VCF2MAF SYMBOL_SOURCE_VCF2MAF HGNC_ID_VCF2MAF BIOTYPE_VCF2MAF CANONICAL_VCF2MAF CCDS_VCF2MAF ENSP_VCF2MAF SWISSPROT_VCF2MAF TREMBL_VCF2MAF UNIPARC_VCF2MAF RefSeq_VCF2MAF SIFT_VCF2MAF PolyPhen_VCF2MAF EXON_VCF2MAF INTRON_VCF2MAF DOMAINS_VCF2MAF AF_VCF2MAF AFR_AF_VCF2MAF AMR_AF_VCF2MAF ASN_AF_VCF2MAF EAS_AF_VCF2MAF EUR_AF_VCF2MAF SAS_AF_VCF2MAF AA_AF_VCF2MAF EA_AF_VCF2MAF CLIN_SIG_VCF2MAF SOMATIC_VCF2MAF PUBMED_VCF2MAF MOTIF_NAME_VCF2MAF MOTIF_POS_VCF2MAF HIGH_INF_POS_VCF2MAF MOTIF_SCORE_CHANGE_VCF2MAF IMPACT_VCF2MAF PICK_VCF2MAF VARIANT_CLASS_VCF2MAF TSL_VCF2MAF HGVS_OFFSET_VCF2MAF PHENO_VCF2MAF MINIMISED_VCF2MAF ExAC_AF_VCF2MAF ExAC_AF_AFR_VCF2MAF ExAC_AF_AMR_VCF2MAF ExAC_AF_EAS_VCF2MAF ExAC_AF_FIN_VCF2MAF ExAC_AF_NFE_VCF2MAF ExAC_AF_OTH_VCF2MAF ExAC_AF_SAS_VCF2MAF GENE_PHENO_VCF2MAF FILTER_VCF2MAF flanking_bps_VCF2MAF vcf_id_VCF2MAF vcf_qual_VCF2MAF ExAC_AF_Adj_VCF2MAF ExAC_AC_AN_Adj_VCF2MAF ExAC_AC_AN_VCF2MAF ExAC_AC_AN_AFR_VCF2MAF ExAC_AC_AN_AMR_VCF2MAF ExAC_AC_AN_EAS_VCF2MAF ExAC_AC_AN_FIN_VCF2MAF ExAC_AC_AN_NFE_VCF2MAF ExAC_AC_AN_OTH_VCF2MAF ExAC_AC_AN_SAS_VCF2MAF ExAC_FILTER_VCF2MAF gnomAD_AF_VCF2MAF gnomAD_AFR_AF_VCF2MAF gnomAD_AMR_AF_VCF2MAF gnomAD_ASJ_AF_VCF2MAF gnomAD_EAS_AF_VCF2MAF gnomAD_FIN_AF_VCF2MAF gnomAD_NFE_AF_VCF2MAF gnomAD_OTH_AF_VCF2MAF gnomAD_SAS_AF_VCF2MAF vcf_pos_VCF2MAF #Uploaded_variation_VEP Location_VEP Allele_VEP Gene_VEP Feature_VEP Feature_type_VEP Consequence_VEP cDNA_position_VEP CDS_position_VEP Protein_position_VEP Amino_acids_VEP Codons_VEP Existing_variation_VEP Extra_VEP IMPACT_VEP STRAND_VEP SYMBOL_VEP SYMBOL_SOURCE_VEP HGNC_ID_VEP BIOTYPE_VEP CANONICAL_VEP CCDS_VEP ENSP_VEP SWISSPROT_VEP UNIPARC_VEP INTRON_VEP HGVSc_VEP AFR_AF_VEP AMR_AF_VEP EAS_AF_VEP EUR_AF_VEP SAS_AF_VEP MAX_AF_VEP MAX_AF_POPS_VEP TREMBL_VEP EXON_VEP HGVSp_VEP gnomAD_AF_VEP gnomAD_AFR_AF_VEP gnomAD_AMR_AF_VEP gnomAD_ASJ_AF_VEP gnomAD_EAS_AF_VEP gnomAD_FIN_AF_VEP gnomAD_NFE_AF_VEP gnomAD_OTH_AF_VEP gnomAD_SAS_AF_VEP HGVS_OFFSET_VEP Tumor_Sample Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Tumor_Sample_Site
0/0 2 11 11,0 11.0 11.0 0.0 0/1 2 6 4,2 6.0 50 PASS FAM131C 348487 . GRCh37 1 16386305 16386306 + Intron INS - - C rs372070031 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 - - c.451+58dup ENST00000375662 FAM131C,intron_variant,,ENST00000375662,NM_182623.2;CLCNKB,downstream_gene_variant,,ENST00000375667,NM_001165945.2;CLCNKB,downstream_gene_variant,,ENST00000375679,NM_000085.4;CLCNKB,downstream_gene_variant,,ENST00000431772,;FAM131C,intron_variant,,ENST00000494078,; C ENSG00000185519 ENST00000375662 Transcript intron_variant rs372070031 1 -1 FAM131C HGNC 26717 protein_coding YES CCDS41270.1 ENSP00000364814 Q96AQ9 UPI000022B016 NM_182623.2 5/6 0.2731 0.3573 0.3581 0.3757 0.5051 MODIFIER 1 insertion PASS GGC rs143272992 50 16386305 rs143272992 1:16386305-16386306 C ENSG00000185519 ENST00000375662.4 Transcript intron_variant - - - - - rs372070031 IMPACT=MODIFIER;STRAND=-1;SYMBOL=FAM131C;SYMBOL_SOURCE=HGNC;HGNC_ID=26717;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS41270.1;ENSP=ENSP00000364814;SWISSPROT=Q96AQ9;UNIPARC=UPI000022B016;INTRON=5/6;HGVSc=ENST00000375662.4:c.451+58dup;AFR_AF=0.2731;AMR_AF=0.3573;EAS_AF=0.3581;EUR_AF=0.3757;SAS_AF=0.5051;MAX_AF=0.5051;MAX_AF_POPS=SAS MODIFIER -1 FAM131C HGNC 26717 protein_coding YES CCDS41270.1 ENSP00000364814 Q96AQ9 UPI000022B016 5/6 ENST00000375662.4:c.451+58dup 0.2731 0.3573 0.3581 0.3757 0.5051 0.5051 SAS TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
0/0 2 6 6,0 6.0 6.0 0.0 0/1 2 6 4,2 6.0 50 PASS ZIC4 84107 . GRCh37 3 147121630 147121631 + Intron DEL TC TC - rs142316820 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 TC TC c.135+120_135+121del ENST00000525172 ZIC4,intron_variant,,ENST00000383075,NM_032153.5;ZIC4,intron_variant,,ENST00000425731,NM_001168379.1;ZIC4,intron_variant,,ENST00000462748,;ZIC4,intron_variant,,ENST00000463250,;ZIC4,intron_variant,,ENST00000473123,;ZIC4,intron_variant,,ENST00000484399,;ZIC1,intron_variant,,ENST00000488404,;ZIC4,intron_variant,,ENST00000491672,NM_001243256.1;ZIC4,intron_variant,,ENST00000525172,NM_001168378.1;ZIC4,upstream_gene_variant,,ENST00000484586,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,; - ENSG00000174963 ENST00000525172 Transcript intron_variant rs142316820 1 -1 ZIC4 HGNC 20393 protein_coding YES CCDS54652.1 ENSP00000435509 Q8N9L1 C9JZU7,C9JD04,C9J6T3,B3KPI4 UPI0001914D88 NM_001168378.1 1/4 MODIFIER 1 deletion 1.0 PASS GATCT . 50 147121629 3_147121630_TC/- 3:147121630-147121631 - ENSG00000174963 ENST00000525172.2 Transcript intron_variant - - - - - rs142316820 IMPACT=MODIFIER;STRAND=-1;SYMBOL=ZIC4;SYMBOL_SOURCE=HGNC;HGNC_ID=20393;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS54652.1;ENSP=ENSP00000435509;SWISSPROT=Q8N9L1;TREMBL=C9JZU7,C9JD04,C9J6T3,B3KPI4;UNIPARC=UPI0001914D88;INTRON=1/4;HGVSc=ENST00000525172.2:c.135+120_135+121del MODIFIER -1 ZIC4 HGNC 20393 protein_coding YES CCDS54652.1 ENSP00000435509 Q8N9L1 UPI0001914D88 1/4 ENST00000525172.2:c.135+120_135+121del C9JZU7,C9JD04,C9J6T3,B3KPI4 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
0/0 2 7 7,0 7.0 7.0 0.0 0/1 2 6 2,4 6.0 50 PASS EIF4G1 1981 . GRCh37 3 184043926 184043927 + Intron DEL AC AC - rs34901174 TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 AC AC c.3243+217_3243+218del ENST00000424196 EIF4G1,intron_variant,,ENST00000319274,;EIF4G1,intron_variant,,ENST00000342981,NM_182917.4;EIF4G1,intron_variant,,ENST00000346169,NM_198241.2;EIF4G1,intron_variant,,ENST00000350481,NM_198242.2;EIF4G1,intron_variant,,ENST00000352767,NM_001194947.1;EIF4G1,intron_variant,,ENST00000382330,NM_001194946.1;EIF4G1,intron_variant,,ENST00000392537,NM_198244.2;EIF4G1,intron_variant,,ENST00000411531,;EIF4G1,intron_variant,,ENST00000414031,;EIF4G1,intron_variant,,ENST00000424196,;EIF4G1,intron_variant,,ENST00000427845,;EIF4G1,intron_variant,,ENST00000434061,NM_004953.4;EIF4G1,intron_variant,,ENST00000435046,;EIF4G1,intron_variant,,ENST00000441154,;EIF2B5,intron_variant,,ENST00000444495,;EIF4G1,intron_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000421110,;EIF4G1,downstream_gene_variant,,ENST00000426123,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000428387,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000450424,;EIF4G1,downstream_gene_variant,,ENST00000457456,;SNORD66,downstream_gene_variant,,ENST00000390856,NR_003055.1;EIF4G1,intron_variant,,ENST00000442406,;EIF4G1,intron_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000464548,;EIF4G1,upstream_gene_variant,,ENST00000475721,;EIF4G1,upstream_gene_variant,,ENST00000482303,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,downstream_gene_variant,,ENST00000493299,; - ENSG00000114867 ENST00000424196 Transcript intron_variant rs34901174 1 1 EIF4G1 HGNC 3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556 UPI00015E0966 20/31 MODIFIER 1 deletion 1.0 PASS AAACA rs112208190 50 184043925 rs112208190 3:184043926-184043927 - ENSG00000114867 ENST00000424196.1 Transcript intron_variant - - - - - rs34901174 IMPACT=MODIFIER;STRAND=1;SYMBOL=EIF4G1;SYMBOL_SOURCE=HGNC;HGNC_ID=3296;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS54687.1;ENSP=ENSP00000416255;SWISSPROT=Q04637;TREMBL=Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556;UNIPARC=UPI00015E0966;INTRON=20/31;HGVSc=ENST00000424196.1:c.3243+217_3243+218del MODIFIER 1 EIF4G1 HGNC 3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 UPI00015E0966 20/31 ENST00000424196.1:c.3243+217_3243+218del Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01
0/0 2 22 22,0 22.0 22.0 0.0 0/1 2 6 4,2 6.0 50 PASS STEAP1B 256227 . GRCh37 7 22533452 22533453 + Frame_Shift_Del DEL CA CA - novel TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 CA CA c.87_88del p.His29GlnfsTer24 p.H29Qfs*24 ENST00000404369 3/5 STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000404369,NM_001164460.1;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000424363,;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000439708,;STEAP1B,intron_variant,,ENST00000406890,NM_207342.2;STEAP1B,splice_region_variant,,ENST00000483679,; - ENSG00000105889 ENST00000404369 Transcript frameshift_variant,splice_region_variant 503-504/1515 87-88/1029 29-30/342 HE/QX caTGag/caag 1 -1 STEAP1B HGNC 41907 protein_coding YES CCDS56469.1 ENSP00000384370 C9JL51,C9JE84,B5MCI2 UPI000173A267 NM_001164460.1 3/5 PANTHER:PTHR14239:SF3,PANTHER:PTHR14239 HIGH 1 deletion PASS CTCAT rs116873396 50 22533451 rs116873396 7:22533452-22533453 - ENSG00000105889 ENST00000404369.4 Transcript frameshift_variant,splice_region_variant 503-504 87-88 29-30 HE/QX caTGag/caag - IMPACT=HIGH;STRAND=-1;SYMBOL=STEAP1B;SYMBOL_SOURCE=HGNC;HGNC_ID=41907;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS56469.1;ENSP=ENSP00000384370;TREMBL=C9JL51,C9JE84,B5MCI2;UNIPARC=UPI000173A267;EXON=3/5;HGVSc=ENST00000404369.4:c.87_88del;HGVSp=ENSP00000384370.4:p.His29GlnfsTer24 HIGH -1 STEAP1B HGNC 41907 protein_coding YES CCDS56469.1 ENSP00000384370 UPI000173A267 ENST00000404369.4:c.87_88del C9JL51,C9JE84,B5MCI2 3/5 ENSP00000384370.4:p.His29GlnfsTer24 TCGA-A1-A0SD TCGA-A1-A0SD-01A-11D-A10Y-09 TCGA-A1-A0SD-10A-01D-A110-09 01